1ZZN

Crystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural evidence for a two-metal-ion mechanism of group I intron splicing.

Stahley, M.R.Strobel, S.A.

(2005) Science 309: 1587-1590

  • DOI: 10.1126/science.1114994

  • PubMed Abstract: 
  • We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordin ...

    We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordination, including the 2'-OH of the terminal guanosine. This structure suggests that, like protein phosphoryltransferases, an RNA phosphoryltransferase can use a two-metal-ion mechanism. Two Mg2+ ions are positioned 3.9 angstroms apart and are directly coordinated by all six of the biochemically predicted ligands. The evolutionary convergence of RNA and protein active sites on the same inorganic architecture highlights the intrinsic chemical capacity of the two-metal-ion catalytic mechanism for phosphoryl transfer.


    Related Citations: 
    • Crystal Structure of a Self-Splicing Group I Intron with Both Exons
      Adams, P.L.,Stahley, M.R.,Kosek, A.B.,Wang, J.,Strobel, S.A.
      (2004) Nature 430: 45
    • In vitro splicing of the ribosomal RNA precursor of tetrahymena: involvement of a guanosine nucleotide in the excision of intervening sequence
      Cech, T.R.,Zaug, A.J.,Grabowaski, P.J.
      (1981) Cell 27: 487
    • Crystal Structure of a group I intron splicing intermediate
      Adams, P.L.,Stahley, M.R.,Gill, M.L.,Kosek, A.B.,Wang, J.,Strobel, S.A.
      (2004) RNA 10: 1867
    • Self-splicing intron in tRNA genes of widely divergent bacteria
      Reinhold-Hurek, B.,Shub, D.A.
      (1992) Nature 357: 173


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN
A
98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
197-MERB197N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP*GP*CP*C)-3'C22N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*AP*(5MU))-3'D3N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
B
RNA LINKINGC10 H13 N5 O9 P2A
GTP
Query on GTP
B
NON-POLYMERC10 H16 N5 O14 P3G
5MU
Query on 5MU
D
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.269 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.466α = 90.00
b = 108.466β = 90.00
c = 246.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description